Yeah I agree with Nelson. Proper grounding in a car stereo system can be a biatch to get perfect. All it takes is an ohm or two of extra resistance on your ground lead and you start getting all kinds of weird sounds in your system. The reason you're probably only hearing it in your subs is because your subs are the only speakers affected by a ground-loop problem. Your surround speakers are driven by the head unit, which most likely has ground-loop isolation circuitry built in.
As an experiment, first try a new RCA cable. If that doesn't fix it, try grounding the outer ring of your RCA cable, i.e. strip a wire and hold one side to the "outside" ring of the RCA cable, and the other side to a good ground in the car. If that still doesn't fix it, try disconnecting the ground cable on your amp and insulate the entire amp (don't let any part of the chassis touch metal in the car). Then run a temporary ground wire directly from the battery to the ground on the amp. If this STILL hasn't fixed the problem, the final thing to try is a ground-loop isolator (you can get them for ~$10 at most car audio shops). It plugs inline on your RCAs and will most likely fix the problem.
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